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Expression Analysis Says Chips, Next-Gen Sequencers ‘Perfect Fit’ in New GWAS Service

Expression Analysis last week launched a new genome-wide association studies service that it expects will help expand its customer base among pharmaceutical companies and academic researchers and ultimately build up a business for the Helicos next-generation sequencing instrument that it purchased last month.
President and CEO Steve McPhail said that Expression Analysis will offer customers a choice of microarray platform — the company is a certified Illumina and Affymetrix service provider — for genome-wide association studies, and will give them the ability to move their studies into the sequencing arena as they narrow their focus to specific regions within the genome.
“We are platform agnostic,” he told BioArray News last week. “We think that all array platforms have their strengths and so we don’t promote one platform over any other.”
Furthermore, Expression Analysis last month ordered the Helicos Biosciences’ Genetic Analysis System in order to begin offering sequencing services — an additional capability that McPhail said could make the firm an attractive partner for the kinds of customers it is trying to reach.
“What we see in most genome-wide association studies is that clients are defining regions of interest using large array capabilities,” McPhail said. “We do think that sequencing represents a perfect fit for follow-up studies to genome-wide association studies. [It’s a] perfect opportunity for our clients to get into fine-level mapping in terms of those specific regions identified in genome-wide association studies.”
Expression Analysis has actually been performing genome-wide association studies for its pharmaceutical clients for several years. However, McPhail said that these clients have been “moving away from disease-association studies and more to drug-response-association studies.” Now, he said, Expression Analysis has an opportunity to channel its experience into reaching more academic customers with its services.
“If you think about genome-wide association studies, they have only been available for two and a half years,” he said. “As the pricing has come down, we have seen a tremendous increase in demand for this kind of testing.”
He acknowledged that many of the academics Expression Analysis is trying to reach may face budget constraints related to performing this magnitude of a study, but said the company’s existing pharmaceutical customers together with newer academic clients enabled the firm to buy consumables at a discount price.

“We think that all array platforms have their strengths and so we don’t promote one platform over any other.”

“We have been able to combine pharma and academic volumes, giving us considerable purchasing power with our vendors [and] allowing us to pass on cost savings to our clients,” he said. He did not discuss pricing for the service or name existing customers.
An Advisory Role
Genome-wide association studies are a component of the $600 million genotyping market. This market, though, has changed over the past few years. New chips have been introduced and the price of arrays has steadily decreased. EA’s program, therefore, is an effort to get more academics, enticed by less work and lower costs, to outsource their projects to the company.
The number of genome-wide association studies is indeed growing. For example, a PubMed search for “genome-wide association” or “whole-genome association“ yielded 194 hits for 2008 so far, compared to 274 in 2007, 97 in 2006, and 66 in 2005.
The extent of EA’s new service is not exactly defined, according to McPhail. Hypothetically, he said, EA is willing to help researchers from experimental design right through the data-analysis process.   
McPhail said that sequencing is an area where EA could especially play an advisory role. “The data that is generated on a typical Affymetrix or Illumina whole-genome chip is somewhere between a gigabyte or two gigabytes. A next-gen sequencer will generate terabytes of data per run. Our clients will then require a significant amount of help with data reduction.”
When it comes to genome-wide association studies, EA has relatively few direct competitors. Both Affymetrix and Illumina offer services, but it is only one component of their businesses. McPhail acknowledged that EA’s new service would compete against Affy’s and Illumina’s service businesses.
The Translational Genomics Institute in Phoenix and the Broad Institute in Cambridge, Mass., also have the capabilities to handle genome-wide association studies, but their business models distinguish them from EA in that they are research institutes looking to collaborate on projects, not privately held businesses seeking to earn a profit.
In this competitive environment, McPhail said that the company will seek to convince prospective customers to use its facilities rather than partner with Affy or Illumina on the basis of cost and efficiency. “From a turnaround-time perspective, our vendors often have significant backlogs and we can often be much more flexible in study prioritization,” McPhail said.
“Also, we have built a quality system that adheres to” Clinical and Laboratory Standards Institute guidelines, Clinical Laboratory Improvement Act guidelines, and Good Laboratory Practice regulations, he said.
Affymetrix’s Clinical Service Laboratory, though, is similarly CLIA-certified and abides by CLSI guidelines. Illumina’s FastTrack genotyping services, however, are not performed in a CLIA-approved environment.
Other possible competition for the service may come from academic core labs. McPhail also argued that academic core labs typically face capacity constraints, a situation that EA hopes will draw more academics into its orbit. “Genome-wide association studies are large studies and typically academic cores don’t have capacity to deal with that volume of specimens,” he said. “We have the capacity to deal with over 70,000 specimens per year. Turnaround time is a huge issue because it allows our academic clients to publish sooner.”

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